By Topic

Computational Biology and Bioinformatics, IEEE/ACM Transactions on

Issue 3 • Date July-Sept. 2006

Filter Results

Displaying Results 1 - 15 of 15
  • [Front cover]

    Publication Year: 2006 , Page(s): c1
    Cited by:  Papers (1)
    Request Permissions | PDF file iconPDF (347 KB)  
    Freely Available from IEEE
  • [Inside front cover]

    Publication Year: 2006 , Page(s): c2
    Request Permissions | PDF file iconPDF (101 KB)  
    Freely Available from IEEE
  • Three-Dimensional Shape-Structure Comparison Method for Protein Classification

    Publication Year: 2006 , Page(s): 193 - 207
    Cited by:  Papers (10)
    Request Permissions | Click to expandAbstract | PDF file iconPDF (2873 KB) |  | HTML iconHTML  

    In this paper, a 3D shape-based approach is presented for the efficient search, retrieval, and classification of protein molecules. The method relies primarily on the geometric 3D structure of the proteins, which is produced from the corresponding PDB files and secondarily on their primary and secondary structure. After proper positioning of the 3D structures, in terms of translation and scaling, ... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • Multiple Peak Alignment in Sequential Data Analysis: A Scale-Space-Based Approach

    Publication Year: 2006 , Page(s): 208 - 219
    Cited by:  Papers (4)
    Request Permissions | Click to expandAbstract | PDF file iconPDF (1487 KB) |  | HTML iconHTML  

    In this paper, we address the multiple peak alignment problem in sequential data analysis with an approach based on the Gaussian scale-space theory. We assume that multiple sets of detected peaks are the observed samples of a set of common peaks. We also assume that the locations of the observed peaks follow unimodal distributions (e.g., normal distribution) with their means equal to the correspon... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • A Powerful Approach for Effective Finding of Significantly Differentially Expressed Genes

    Publication Year: 2006 , Page(s): 220 - 231
    Request Permissions | Click to expandAbstract | PDF file iconPDF (1472 KB) |  | HTML iconHTML  

    The problem of identifying significantly differentially expressed genes for replicated microarray experiments is accepted as significant and has been tackled by several researchers. Patterns from gene expression (PaGE) and q-values are two of the well-known approaches developed to handle this problem. This paper proposes a powerful approach to handle this problem. We first propose a method for est... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • Correlation Statistics for cDNA Microarray Image Analysis

    Publication Year: 2006 , Page(s): 232 - 238
    Cited by:  Papers (5)
    Request Permissions | Click to expandAbstract | PDF file iconPDF (1761 KB) |  | HTML iconHTML  

    In this paper, correlation of the pixels comprising a microarray spot is investigated. Subsequently, correlation statistics, namely, Pearson correlation and Spearman rank correlation, are used to segment the foreground and background intensity of microarray spots. The performance of correlation-based segmentation is compared to clustering-based (PAM, k-means) and seeded-region growing techniques (... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • Counting All Possible Ancestral Configurations of Sample Sequences in Population Genetics

    Publication Year: 2006 , Page(s): 239 - 251
    Cited by:  Papers (1)
    Request Permissions | Click to expandAbstract | PDF file iconPDF (2072 KB) |  | HTML iconHTML  

    Given a set D of input sequences, a genealogy for D can be constructed backward in time using such evolutionary events as mutation, coalescent, and recombination. An ancestral configuration (AC) can be regarded as the multiset of all sequences present at a particular point in time in a possible genealogy for D. The complexity of computing the likelihood of observing D depends heavily on the total ... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • Finding Consistent Gene Transmission Patterns on Large and Complex Pedigrees

    Publication Year: 2006 , Page(s): 252 - 262
    Request Permissions | Click to expandAbstract | PDF file iconPDF (2346 KB) |  | HTML iconHTML  

    A heuristic algorithm for finding gene transmission patterns on large and complex pedigrees with partially observed genotype data is proposed. The method can be used to generate an initial point for a Markov chain Monte Carlo simulation or to check that the given pedigree and the genotype data are consistent. In small pedigrees, the algorithm is exact by exhaustively enumerating all possibilities,... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • Fuzzy Measures on the Gene Ontology for Gene Product Similarity

    Publication Year: 2006 , Page(s): 263 - 274
    Cited by:  Papers (35)
    Request Permissions | Click to expandAbstract | PDF file iconPDF (2288 KB) |  | HTML iconHTML  

    One of the most important objects in bioinformatics is a gene product (protein or RNA). For many gene products, functional information is summarized in a set of gene ontology (GO) annotations. For these genes, it is reasonable to include similarity measures based on the terms found in the GO or other taxonomy. In this paper, we introduce several novel measures for computing the similarity of two g... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • Genome Rearrangement Based on Reversals that Preserve Conserved Intervals

    Publication Year: 2006 , Page(s): 275 - 288
    Cited by:  Papers (2)
    Request Permissions | Click to expandAbstract | PDF file iconPDF (2841 KB) |  | HTML iconHTML  

    The order of genes in the genomes of species can change during evolution and can provide information about their phylogenetic relationship. An interesting method to infer the phylogenetic relationship from the gene orders is to use different types of rearrangement operations and to find possible rearrangement scenarios using these operations. One of the most common rearrangement operations is reve... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • Improved Parameterized Complexity of the Maximum Agreement Subtree and Maximum Compatible Tree Problems

    Publication Year: 2006 , Page(s): 289 - 302
    Cited by:  Papers (2)
    Request Permissions | Click to expandAbstract | PDF file iconPDF (341 KB) |  | HTML iconHTML  

    Given a set of evolutionary trees on a same set of taxa, the maximum agreement subtree problem (MAST), respectively, maximum compatible tree problem (MCT), consists of finding a largest subset of taxa such that all input trees restricted to these taxa are isomorphic, respectively compatible. These problems have several applications in phylogenetics such as the computation of a consensus of phyloge... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • Islands of Tractability for Parsimony Haplotyping

    Publication Year: 2006 , Page(s): 303 - 311
    Cited by:  Papers (7)
    Request Permissions | Click to expandAbstract | PDF file iconPDF (825 KB) |  | HTML iconHTML  

    We study the parsimony approach to haplotype inference, which calls for finding a set of haplotypes of minimum cardinality that explains an input set of genotypes. We prove that the problem is APX-hard even in very restricted cases. On the positive side, we identify islands of tractability for the problem, by focusing on instances with specific structure of haplotype sharing among the input genoty... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • Significance of Gene Ranking for Classification of Microarray Samples

    Publication Year: 2006 , Page(s): 312 - 320
    Cited by:  Papers (9)
    Request Permissions | Click to expandAbstract | PDF file iconPDF (1777 KB) |  | HTML iconHTML  

    Many methods for classification and gene selection with microarray data have been developed. These methods usually give a ranking of genes. Evaluating the statistical significance of the gene ranking is important for understanding the results and for further biological investigations, but this question has not been well addressed for machine learning methods in existing works. Here, we address thi... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • IEEE/ACM TCBB: Information for authors

    Publication Year: 2006 , Page(s): c3
    Request Permissions | PDF file iconPDF (101 KB)  
    Freely Available from IEEE
  • [Back cover]

    Publication Year: 2006 , Page(s): c4
    Request Permissions | PDF file iconPDF (347 KB)  
    Freely Available from IEEE

Aims & Scope

This bimonthly publishes archival research results related to the algorithmic, mathematical, statistical, and computational methods that are central in bioinformatics and computational biology.

Full Aims & Scope

Meet Our Editors

Editor-in-Chief
Ying Xu
University of Georgia
xyn@bmb.uga.edu

Associate Editor-in-Chief
Dong Xu
University of Missouri
xudong@missouri.edu